Water, protons, and ions play a central role in the stability, dynamics, and function of biomolecules. Through the hydrophobic effect and hydrogen bond interactions, water is a major factor in the folding of proteins. In many enzymes, it participates directly in the catalytic function. In particular, water in the protein interior often mediates the transfer of protons between the solvent medium and the active site. Such water, often confined into relatively nonpolar pores and cavities of nanoscopic dimensions, exhibits highly unusual properties, such as high water mobility, high proton conductivity, or sharp transitions between filled and empty states. Proteins exploit these unusual properties of confined water in their biological function, e.g., to ensure rapid water flow in aquaporins, or to gate proton flow in proton pumps and enzymes. Function of cytochrome c oxidase. Aerobic life is based on a molecular machinery that utilizes oxygen as a terminal electron sink. The membrane-bound cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water in mitochondria and many bacteria. The energy released in this reaction is conserved by pumping protons across the mitochondrial or bacterial membrane, creating an electrochemical proton gradient that drives production of ATP. In collaboration with Dr. Wikstrom (University of Helsinki, Finland) we have developed a detailed kinetic model of the redox-coupled proton pump in CcO (Kim et al., Proc. Natl. Acad. Sci. USA 2009). The model is consistent with thermodynamic principles, the structure of CcO, experimentally known proton affinities, and equilibrium constants of intermediate reactions. The high pumping efficiency of CcO requires strong electrostatic couplings between the proton loading (pump) site and the electron site (heme a), and kinetic gating of the internal proton transfer. Gating is achieved by enhancing the rate of proton transfer from the conserved Glu-242 to the pump site on reduction of heme a, consistent with the predictions of our water-gated model of proton pumping. In collaboration with Drs. Kaila and Wikstrom (University of Helsinki, Finland) we explored by molecular dynamics simulations how the protons pumped by CcO are prevented from flowing backwards during the process (Kaila et al., Biochim. Biophys. Acta Bioenerg. 2009). We have studied the function of Glu242 (bovine numbering) as a proton valve by exploring how the redox state of the surrounding metal centers, dielectric effects, and membrane potential, affect the energetics of charge motion. Ribonuclease H function. We have studied the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans (Rosta et al., J. Comput. Chem. 2009). This protein is a close relative of the RNaseH of the HIV virus. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used in this work to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free energy calculations. 1D water wires: In collaboration with Drs. Dellago and Kofinger from the University of Vienna, Austria, we performed studies of one-dimensional water wires. Such wires are important elements of biological water channels and proton conduction wires in proteins. We developed a detailed dipole lattice model and showed that it accurately recovers key properties of 1D confined water when compared to atomically detailed simulations (Kofinger et al, J. Chem. Phys. 2009). Water in nanoconfinement and at interfaces: In collaboration with Dr. Mittal (LCP, NIDDK) we have studied the static and dynamic properties of water near extended nonpolar surfaces (Proc. Natl. Acad. Sci. USA, 2008). With the help of extensive molecular dynamics simulations, we showed that for large solutes, the interfacial density profile is broadened by capillary waves. The apparent interfacial tension extracted from the width of the density profiles agrees with that of a free liquid-vapor interface. These results shed new light on the role of water in molecular binding and recognition processes, and provide important guidance for the development of accurate theories to describe water-mediated interactions.